A novel micro-solid phase extraction (microSPE) device was prepared by electrochemically adhering molecularly imprinted polypyrrole encapsulated carbon nanotubes (MIPPy/CNTs) onto a stainless steel frit. It was found that the use of CNTs increased the total binding capacity without compromising the porosity of the frit. Three templates, 17alpha-ethynyl estradiol (EE2), 17beta-estradiol (E2), and ochratoxin A (OTA) were imprinted individually to make their respective MIPPy/CNTs-modified frits. The binding properties of these microSPE devices were characterized by high performance liquid chromatography (HPLC) with fluorescence detection (FLD). In comparison with non-imprinted polypyrrole encapsulated carbon nanotubes (PPy/CNTs), the molecular imprinting technique enhanced the selective binding towards the imprint molecules. MIPPy/CNTs-microSPE-HPLC-FLD results demonstrated the selectivity of MIPPy had been tailored by imprinting with different templates. This is the first report on how versatile pyrrole can be as a functional monomer for the molecular imprinting of target compounds with a broad range of high to low pKa values.